Optical scanners have been developed that are capable of generating a three-dimensional image of a physical object or a real-world environment. While limited three-dimensional modeling is possible based on a single scan of the subject, more thorough modeling can be achieved using multiple scans. Multiple scans can be acquired by simultaneously scanning the subject with multiple cameras from different perspectives, or alternatively, by sequentially scanning the subject with a single camera which is moved between scans. In some applications, tens, hundreds, or even thousands of scans may be acquired, depending on the level of detail required in a given application. Once acquired, these multiple scans are brought into a common reference system in a process that is typically referred to as “global alignment”, “multi-view alignment”, or “registration”. In theory, a pair of perfectly calibrated scans could be aligned using a rigid transformation that consists only of translation and rotation. However, as a practical matter, even calibrated scans contain non-rigid distortions due to the accumulation of tracking errors and nonlinear measurement distortions in optical sensors. More significant non-rigid distortions occur when the subject being scanned moves slightly (such as in the case of scanning a living person who is breathing) or when the scanner is moved erratically (such as in the case of a handheld camera). These non-rigid distortions can cause loss of high-frequency details in the resulting three-dimensional image. To counter this, techniques have been developed for “global non-rigid alignment” of three-dimensional scans. One such technique in disclosed by Brown, et al., “Global Non-Rigid Alignment of 3-D Scans”, ACM Transactions on Graphics (Proceedings of ACM SIGGRAPH 2007), Vol. 26, No. 3, Article 21 (July 2007) (hereinafter referred to as “Brown, et al.”).